Multiple sequence alignment - TraesCS2B01G094600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G094600 chr2B 100.000 3161 0 0 1 3161 54732406 54735566 0.000000e+00 5838
1 TraesCS2B01G094600 chr2D 86.982 3303 239 93 7 3161 32960940 32964199 0.000000e+00 3541
2 TraesCS2B01G094600 chr2A 90.417 1534 98 19 464 1964 36119479 36120996 0.000000e+00 1973
3 TraesCS2B01G094600 chr2A 91.057 984 73 9 954 1924 35469064 35468083 0.000000e+00 1315
4 TraesCS2B01G094600 chr2A 84.267 1214 111 35 1948 3106 36121106 36122294 0.000000e+00 1110
5 TraesCS2B01G094600 chr2A 83.832 334 35 6 1 327 36119159 36119480 1.840000e-77 300
6 TraesCS2B01G094600 chrUn 90.555 1027 79 10 954 1964 280377632 280376608 0.000000e+00 1343
7 TraesCS2B01G094600 chrUn 84.349 1214 108 35 1948 3106 280376498 280375312 0.000000e+00 1114


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G094600 chr2B 54732406 54735566 3160 False 5838.000000 5838 100.000 1 3161 1 chr2B.!!$F1 3160
1 TraesCS2B01G094600 chr2D 32960940 32964199 3259 False 3541.000000 3541 86.982 7 3161 1 chr2D.!!$F1 3154
2 TraesCS2B01G094600 chr2A 35468083 35469064 981 True 1315.000000 1315 91.057 954 1924 1 chr2A.!!$R1 970
3 TraesCS2B01G094600 chr2A 36119159 36122294 3135 False 1127.666667 1973 86.172 1 3106 3 chr2A.!!$F1 3105
4 TraesCS2B01G094600 chrUn 280375312 280377632 2320 True 1228.500000 1343 87.452 954 3106 2 chrUn.!!$R1 2152

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
125 139 0.176449 TCGGCACATGTCCTGATGAG 59.824 55.0 0.00 0.0 0.00 2.90 F
1674 1749 0.179004 TGTGGGCTTTCGACACCATT 60.179 50.0 1.19 0.0 35.13 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2217 1.394917 GAAATCGCAATCGTCAGCACT 59.605 47.619 0.00 0.0 36.96 4.40 R
3003 3296 0.034767 ATGTGCACCAGACCAGATGG 60.035 55.000 15.69 0.0 43.87 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.668280 GCGCGGTGTTCTTCTCCAC 61.668 63.158 8.83 0.00 0.00 4.02
75 82 0.899720 AAAACTGCATCATGCCCCAG 59.100 50.000 7.30 0.00 44.23 4.45
76 83 0.251922 AAACTGCATCATGCCCCAGT 60.252 50.000 7.30 0.60 44.23 4.00
77 84 0.968901 AACTGCATCATGCCCCAGTG 60.969 55.000 7.30 0.00 44.23 3.66
78 85 2.043752 TGCATCATGCCCCAGTGG 60.044 61.111 7.30 0.63 44.23 4.00
115 129 3.781079 ATTTGGTTATGTCGGCACATG 57.219 42.857 0.00 0.00 43.54 3.21
125 139 0.176449 TCGGCACATGTCCTGATGAG 59.824 55.000 0.00 0.00 0.00 2.90
161 175 2.561569 ACCCTTTGCGCATATAGTGAC 58.438 47.619 12.75 0.00 0.00 3.67
181 195 2.763448 ACAGATGAGAAGGCTGTCCTAC 59.237 50.000 0.00 0.00 43.40 3.18
196 211 5.049336 GCTGTCCTACTTTTTCTGTTTCCTC 60.049 44.000 0.00 0.00 0.00 3.71
254 269 6.869315 TTTTTAGTATGCTGTGCTTGTACA 57.131 33.333 0.00 0.00 0.00 2.90
268 283 4.025563 TGCTTGTACACGTGTTGTTGTATC 60.026 41.667 28.55 9.33 39.91 2.24
269 284 4.210537 GCTTGTACACGTGTTGTTGTATCT 59.789 41.667 28.55 0.00 39.91 1.98
270 285 5.277154 GCTTGTACACGTGTTGTTGTATCTT 60.277 40.000 28.55 0.00 39.91 2.40
271 286 5.644902 TGTACACGTGTTGTTGTATCTTG 57.355 39.130 28.55 0.00 39.91 3.02
272 287 5.110598 TGTACACGTGTTGTTGTATCTTGT 58.889 37.500 28.55 0.00 39.91 3.16
273 288 6.271566 TGTACACGTGTTGTTGTATCTTGTA 58.728 36.000 28.55 0.00 39.91 2.41
274 289 6.924612 TGTACACGTGTTGTTGTATCTTGTAT 59.075 34.615 28.55 0.00 39.91 2.29
302 317 6.667414 ACCTAATTATTCAATTTCCCAGTGCA 59.333 34.615 0.00 0.00 35.88 4.57
347 362 2.342651 CGAGAACATCGTGTCATGTGAC 59.657 50.000 6.21 6.21 46.62 3.67
370 385 0.676782 CTTTTTCAGCGGACGGGGAT 60.677 55.000 0.00 0.00 0.00 3.85
403 418 5.869344 GCAGACGCCAGATATACATCATTTA 59.131 40.000 0.00 0.00 33.21 1.40
404 419 6.536582 GCAGACGCCAGATATACATCATTTAT 59.463 38.462 0.00 0.00 33.21 1.40
405 420 7.706607 GCAGACGCCAGATATACATCATTTATA 59.293 37.037 0.00 0.00 33.21 0.98
436 451 5.627182 ATGTACTCATCAGGATGCTTCTT 57.373 39.130 4.39 0.00 38.65 2.52
439 454 4.774660 ACTCATCAGGATGCTTCTTCAT 57.225 40.909 4.39 0.00 38.65 2.57
440 455 4.452825 ACTCATCAGGATGCTTCTTCATG 58.547 43.478 4.39 0.00 38.65 3.07
456 471 1.701292 TCATGCCATATAGCCAGCTGT 59.299 47.619 13.81 0.00 0.00 4.40
530 545 9.402320 TCTACTCTATTCTGAGCCACATATATC 57.598 37.037 0.00 0.00 37.58 1.63
541 583 6.328934 TGAGCCACATATATCCCTAAACTTCA 59.671 38.462 0.00 0.00 0.00 3.02
786 832 8.004344 CGTTTAAATAGGAGAATATGAACTGCG 58.996 37.037 0.00 0.00 0.00 5.18
813 859 7.112779 CCTGGGGTAATTAGAGCTATTTATGG 58.887 42.308 0.00 0.00 0.00 2.74
820 866 9.998106 GTAATTAGAGCTATTTATGGGAGACAA 57.002 33.333 0.00 0.00 0.00 3.18
924 975 8.122952 CGAAGATTTTGTGGGTATCTTGTTATC 58.877 37.037 0.00 0.00 38.40 1.75
931 982 4.689345 GTGGGTATCTTGTTATCGTATGGC 59.311 45.833 0.00 0.00 0.00 4.40
1018 1080 3.022557 ACATGGATCCCAACATGAAGG 57.977 47.619 14.93 0.00 45.55 3.46
1177 1239 5.600069 TGTGTATGATCAGCTAGTGGAGAAT 59.400 40.000 0.09 0.00 0.00 2.40
1252 1314 4.142249 GCCAAGACAACTAAAACCAGTGTT 60.142 41.667 0.00 0.00 35.82 3.32
1253 1315 5.339990 CCAAGACAACTAAAACCAGTGTTG 58.660 41.667 0.00 0.00 43.55 3.33
1283 1345 6.763135 TCCATTTGAGATCGTAATGAAAGAGG 59.237 38.462 14.91 1.46 32.36 3.69
1330 1392 5.929415 GCTAGTAAAGGAGATATGCTCAACC 59.071 44.000 0.00 0.00 45.81 3.77
1357 1419 2.185004 ATCACGACCCCAAAGAACAG 57.815 50.000 0.00 0.00 0.00 3.16
1373 1435 4.729868 AGAACAGACCTGGCTAATGTTTT 58.270 39.130 0.00 0.00 34.41 2.43
1381 1443 2.083774 TGGCTAATGTTTTCAGGCTCG 58.916 47.619 0.00 0.00 35.95 5.03
1414 1476 3.669536 TCGTGTTCCATTTCATGTAGCA 58.330 40.909 0.00 0.00 0.00 3.49
1440 1502 5.891551 ACACTGTTCTGGACAAAGGTATTTT 59.108 36.000 0.00 0.00 37.93 1.82
1571 1634 8.323567 AGGTGGATCATGCTTTCAAATTTATTT 58.676 29.630 0.00 0.00 0.00 1.40
1668 1743 2.673368 CTCAAGTATGTGGGCTTTCGAC 59.327 50.000 0.00 0.00 0.00 4.20
1674 1749 0.179004 TGTGGGCTTTCGACACCATT 60.179 50.000 1.19 0.00 35.13 3.16
1690 1765 5.376625 ACACCATTGACATGTGAAGTAGTT 58.623 37.500 1.15 0.00 0.00 2.24
1691 1766 5.470098 ACACCATTGACATGTGAAGTAGTTC 59.530 40.000 1.15 3.15 0.00 3.01
1695 1770 5.673337 TTGACATGTGAAGTAGTTCTTGC 57.327 39.130 1.15 3.20 36.40 4.01
1714 1794 2.703536 TGCAGTCCCTGTCTGTTCTAAA 59.296 45.455 0.00 0.00 35.60 1.85
1730 1810 9.066892 TCTGTTCTAAACTTGCATTTTATCTGT 57.933 29.630 0.00 0.00 0.00 3.41
1744 1824 8.897752 GCATTTTATCTGTAACCTCTTCTGAAT 58.102 33.333 0.00 0.00 0.00 2.57
1795 1876 2.165030 GCTTGTTTAGCCAGATGCATGT 59.835 45.455 2.46 0.00 44.48 3.21
1801 1882 6.331845 TGTTTAGCCAGATGCATGTTTTATG 58.668 36.000 2.46 0.00 44.83 1.90
1806 1888 4.563976 GCCAGATGCATGTTTTATGTTCAC 59.436 41.667 2.46 0.00 40.77 3.18
1811 1893 8.166066 CAGATGCATGTTTTATGTTCACAAATG 58.834 33.333 2.46 0.00 0.00 2.32
1815 1897 6.957077 GCATGTTTTATGTTCACAAATGATGC 59.043 34.615 0.00 0.00 33.85 3.91
1829 1911 4.635699 AATGATGCCTCTGATGCTCATA 57.364 40.909 14.79 0.00 31.20 2.15
1830 1912 4.635699 ATGATGCCTCTGATGCTCATAA 57.364 40.909 13.66 0.00 30.31 1.90
1916 2002 7.637709 GGACTGTTTCCATTTTAATGTTCAC 57.362 36.000 2.13 0.00 45.10 3.18
1924 2010 8.830201 TTCCATTTTAATGTTCACAATTGGAG 57.170 30.769 10.83 1.96 34.60 3.86
1931 2017 5.796424 ATGTTCACAATTGGAGCTCTTTT 57.204 34.783 14.64 2.13 0.00 2.27
1933 2019 6.707440 TGTTCACAATTGGAGCTCTTTTTA 57.293 33.333 14.64 0.00 0.00 1.52
1946 2161 6.013842 AGCTCTTTTTATTTGAACCCTTCG 57.986 37.500 0.00 0.00 0.00 3.79
1951 2166 8.091385 TCTTTTTATTTGAACCCTTCGACTAC 57.909 34.615 0.00 0.00 0.00 2.73
1955 2170 8.483307 TTTATTTGAACCCTTCGACTACATAC 57.517 34.615 0.00 0.00 0.00 2.39
1987 2225 3.594134 AGCTTGTTGAGATAGTGCTGAC 58.406 45.455 0.00 0.00 0.00 3.51
1993 2231 2.814269 TGAGATAGTGCTGACGATTGC 58.186 47.619 0.00 0.00 0.00 3.56
1997 2235 2.293677 TAGTGCTGACGATTGCGATT 57.706 45.000 0.00 0.00 41.64 3.34
2007 2245 2.166007 CGATTGCGATTTCCAAACGAC 58.834 47.619 0.00 0.00 39.74 4.34
2008 2246 2.412195 CGATTGCGATTTCCAAACGACA 60.412 45.455 0.00 0.00 39.74 4.35
2022 2260 2.071688 ACGACACAGATCAAGAGCAC 57.928 50.000 0.00 0.00 0.00 4.40
2049 2287 0.882042 ACGACACCAAGAAGCTGCAG 60.882 55.000 10.11 10.11 0.00 4.41
2194 2432 1.035139 AAGGGGCGAATGAATCATGC 58.965 50.000 0.00 0.00 0.00 4.06
2271 2509 3.058501 GGGTTCACCAATCGTGTTTACTG 60.059 47.826 0.00 0.00 43.51 2.74
2278 2516 3.067106 CAATCGTGTTTACTGACAGCCT 58.933 45.455 1.25 0.00 0.00 4.58
2298 2539 3.818773 CCTTGATGTTTTACCCGTGTCTT 59.181 43.478 0.00 0.00 0.00 3.01
2300 2541 3.811083 TGATGTTTTACCCGTGTCTTGT 58.189 40.909 0.00 0.00 0.00 3.16
2303 2544 4.619437 TGTTTTACCCGTGTCTTGTTTC 57.381 40.909 0.00 0.00 0.00 2.78
2326 2567 0.592637 TTTGCCGTGCTGTGAGATTG 59.407 50.000 0.00 0.00 0.00 2.67
2354 2595 2.243407 GCTACGAACGAGAGAAGTGTG 58.757 52.381 0.14 0.00 0.00 3.82
2362 2603 1.530031 CGAGAGAAGTGTGGTCGATCG 60.530 57.143 9.36 9.36 32.32 3.69
2425 2666 1.072505 GGCAAACCGGAGTCCTGAA 59.927 57.895 9.46 0.00 0.00 3.02
2440 2681 1.545651 CCTGAACCTGAACCTGTTCCC 60.546 57.143 7.51 0.00 40.06 3.97
2441 2682 0.476771 TGAACCTGAACCTGTTCCCC 59.523 55.000 7.51 0.00 40.06 4.81
2455 2696 3.381335 TGTTCCCCTACCCTGTTATCTC 58.619 50.000 0.00 0.00 0.00 2.75
2461 2702 3.973973 CCCTACCCTGTTATCTCCATTCA 59.026 47.826 0.00 0.00 0.00 2.57
2462 2703 4.599241 CCCTACCCTGTTATCTCCATTCAT 59.401 45.833 0.00 0.00 0.00 2.57
2559 2808 0.687098 TATACGGTGGGCGGGAAAGA 60.687 55.000 0.00 0.00 0.00 2.52
2592 2842 6.100004 TCTCTTGGATGACACGTTTATCTTC 58.900 40.000 0.00 0.00 0.00 2.87
2602 2852 2.224784 ACGTTTATCTTCGGTTTGTGGC 59.775 45.455 0.00 0.00 0.00 5.01
2615 2865 3.674753 GGTTTGTGGCGAATCTGAAATTG 59.325 43.478 0.00 0.00 0.00 2.32
2621 2871 3.171277 GGCGAATCTGAAATTGAAACGG 58.829 45.455 0.00 0.00 0.00 4.44
2641 2891 0.958382 TGGTTTCCATGCGCAGGTAC 60.958 55.000 21.79 18.62 0.00 3.34
2657 2910 5.563085 CGCAGGTACTAGATATGAAGGACAC 60.563 48.000 0.00 0.00 36.02 3.67
2821 3104 1.152546 GCCTTTTGGTGTGAGGGGT 60.153 57.895 0.00 0.00 42.99 4.95
2822 3105 1.463553 GCCTTTTGGTGTGAGGGGTG 61.464 60.000 0.00 0.00 42.99 4.61
2823 3106 0.184933 CCTTTTGGTGTGAGGGGTGA 59.815 55.000 0.00 0.00 34.07 4.02
2826 3111 1.715019 TTTGGTGTGAGGGGTGAGGG 61.715 60.000 0.00 0.00 0.00 4.30
2972 3261 1.676967 GCTGGCTGGCTGTAGCTTT 60.677 57.895 9.69 0.00 43.22 3.51
3002 3295 3.015327 GCCATTCTTCTTCTGTCTGCAT 58.985 45.455 0.00 0.00 0.00 3.96
3003 3296 3.065095 GCCATTCTTCTTCTGTCTGCATC 59.935 47.826 0.00 0.00 0.00 3.91
3004 3297 3.626670 CCATTCTTCTTCTGTCTGCATCC 59.373 47.826 0.00 0.00 0.00 3.51
3005 3298 4.259356 CATTCTTCTTCTGTCTGCATCCA 58.741 43.478 0.00 0.00 0.00 3.41
3007 3300 4.134379 TCTTCTTCTGTCTGCATCCATC 57.866 45.455 0.00 0.00 0.00 3.51
3008 3301 3.773667 TCTTCTTCTGTCTGCATCCATCT 59.226 43.478 0.00 0.00 0.00 2.90
3009 3302 3.538634 TCTTCTGTCTGCATCCATCTG 57.461 47.619 0.00 0.00 0.00 2.90
3010 3303 2.169978 TCTTCTGTCTGCATCCATCTGG 59.830 50.000 0.00 0.00 0.00 3.86
3020 3320 0.254178 ATCCATCTGGTCTGGTGCAC 59.746 55.000 8.80 8.80 35.19 4.57
3027 3327 0.106769 TGGTCTGGTGCACATTGTGT 60.107 50.000 20.43 0.00 35.75 3.72
3106 3407 0.332632 TTCTGGGAGGAGGGCAATTG 59.667 55.000 0.00 0.00 0.00 2.32
3108 3409 2.830370 GGGAGGAGGGCAATTGCG 60.830 66.667 23.48 0.00 43.26 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.928727 TGAACTGTAACACGTAGAGGG 57.071 47.619 0.00 0.00 0.00 4.30
75 82 8.311109 ACCAAATTAACAAATTGTATCTCCCAC 58.689 33.333 0.00 0.00 0.00 4.61
76 83 8.429237 ACCAAATTAACAAATTGTATCTCCCA 57.571 30.769 0.00 0.00 0.00 4.37
85 99 7.116948 TGCCGACATAACCAAATTAACAAATTG 59.883 33.333 0.00 0.00 0.00 2.32
105 119 0.108186 TCATCAGGACATGTGCCGAC 60.108 55.000 14.38 0.00 0.00 4.79
115 129 5.233988 GGTTGTATCTATGCTCATCAGGAC 58.766 45.833 0.00 0.00 0.00 3.85
125 139 3.577805 AGGGTTGGGTTGTATCTATGC 57.422 47.619 0.00 0.00 0.00 3.14
161 175 3.030291 AGTAGGACAGCCTTCTCATCTG 58.970 50.000 0.00 0.00 43.90 2.90
181 195 9.057089 ACAATACTAGTGAGGAAACAGAAAAAG 57.943 33.333 5.39 0.00 0.00 2.27
242 257 1.663643 ACAACACGTGTACAAGCACAG 59.336 47.619 23.69 6.11 39.29 3.66
254 269 6.366877 GGTACATACAAGATACAACAACACGT 59.633 38.462 0.00 0.00 0.00 4.49
273 288 9.936329 ACTGGGAAATTGAATAATTAGGTACAT 57.064 29.630 0.00 0.00 35.50 2.29
274 289 9.184523 CACTGGGAAATTGAATAATTAGGTACA 57.815 33.333 0.00 0.00 35.50 2.90
302 317 8.414003 TCGTCTCTACATCATACTAGCAAAATT 58.586 33.333 0.00 0.00 0.00 1.82
352 367 0.958382 CATCCCCGTCCGCTGAAAAA 60.958 55.000 0.00 0.00 0.00 1.94
370 385 1.206849 TCTGGCGTCTGCATTATGACA 59.793 47.619 0.00 1.35 45.35 3.58
403 418 7.241628 TCCTGATGAGTACATAGACATGGTAT 58.758 38.462 0.00 0.00 36.82 2.73
404 419 6.610830 TCCTGATGAGTACATAGACATGGTA 58.389 40.000 0.00 0.00 36.82 3.25
405 420 5.458595 TCCTGATGAGTACATAGACATGGT 58.541 41.667 0.00 0.00 36.82 3.55
420 435 3.211865 GCATGAAGAAGCATCCTGATGA 58.788 45.455 11.23 0.00 41.20 2.92
440 455 1.972872 AACACAGCTGGCTATATGGC 58.027 50.000 19.93 1.74 42.18 4.40
530 545 3.909732 TGGGCCATAATGAAGTTTAGGG 58.090 45.455 0.00 0.00 36.37 3.53
541 583 3.455177 TCAATGTTGCAATGGGCCATAAT 59.545 39.130 21.54 1.17 43.89 1.28
786 832 1.141185 AGCTCTAATTACCCCAGGCC 58.859 55.000 0.00 0.00 0.00 5.19
820 866 8.621286 CACTAAACACACAAAAATAGGAGACTT 58.379 33.333 0.00 0.00 43.67 3.01
924 975 9.944663 ACTTAATAAAAATACATGTGCCATACG 57.055 29.630 9.11 0.00 0.00 3.06
966 1017 5.163874 GCAAAACAATGTCAACTGCTTTTCA 60.164 36.000 0.00 0.00 0.00 2.69
967 1018 5.163874 TGCAAAACAATGTCAACTGCTTTTC 60.164 36.000 9.30 0.00 0.00 2.29
968 1019 4.694509 TGCAAAACAATGTCAACTGCTTTT 59.305 33.333 9.30 0.00 0.00 2.27
969 1020 4.252073 TGCAAAACAATGTCAACTGCTTT 58.748 34.783 9.30 0.00 0.00 3.51
971 1022 3.119029 ACTGCAAAACAATGTCAACTGCT 60.119 39.130 9.30 0.00 0.00 4.24
972 1023 3.189285 ACTGCAAAACAATGTCAACTGC 58.811 40.909 0.00 0.00 0.00 4.40
973 1024 5.783100 AAACTGCAAAACAATGTCAACTG 57.217 34.783 0.00 0.00 0.00 3.16
974 1025 7.386299 TGTTAAAACTGCAAAACAATGTCAACT 59.614 29.630 0.00 0.00 0.00 3.16
975 1026 7.513968 TGTTAAAACTGCAAAACAATGTCAAC 58.486 30.769 0.00 0.00 0.00 3.18
1018 1080 3.055530 TCAATCAGAGTCCCTTGAAGCTC 60.056 47.826 0.00 0.00 0.00 4.09
1177 1239 5.012458 CCTGTTAGCATTCCTCATCCTATCA 59.988 44.000 0.00 0.00 0.00 2.15
1283 1345 1.981256 TTGGCAGAAGTTCCTTCCAC 58.019 50.000 0.00 0.00 40.98 4.02
1330 1392 2.511600 GGGTCGTGATTCCCGCAG 60.512 66.667 0.00 0.00 33.97 5.18
1357 1419 2.164422 GCCTGAAAACATTAGCCAGGTC 59.836 50.000 0.00 0.00 44.58 3.85
1373 1435 3.206150 GAGCAAAAATATCCGAGCCTGA 58.794 45.455 0.00 0.00 0.00 3.86
1381 1443 4.695217 TGGAACACGAGCAAAAATATCC 57.305 40.909 0.00 0.00 0.00 2.59
1414 1476 2.026262 ACCTTTGTCCAGAACAGTGTGT 60.026 45.455 0.00 0.00 39.58 3.72
1571 1634 7.709182 CCTCATATCGGATTAACAACACAAGTA 59.291 37.037 0.00 0.00 0.00 2.24
1574 1637 6.411376 ACCTCATATCGGATTAACAACACAA 58.589 36.000 0.00 0.00 0.00 3.33
1624 1687 7.967854 TGAGCTCAACATAATTTTCGGTAAATG 59.032 33.333 15.67 0.00 36.57 2.32
1628 1691 6.653320 ACTTGAGCTCAACATAATTTTCGGTA 59.347 34.615 25.16 0.00 0.00 4.02
1638 1713 4.769688 CCCACATACTTGAGCTCAACATA 58.230 43.478 25.16 19.23 0.00 2.29
1668 1743 5.702670 AGAACTACTTCACATGTCAATGGTG 59.297 40.000 0.00 0.00 38.19 4.17
1674 1749 4.702831 TGCAAGAACTACTTCACATGTCA 58.297 39.130 0.00 0.00 36.61 3.58
1714 1794 7.885399 AGAAGAGGTTACAGATAAAATGCAAGT 59.115 33.333 0.00 0.00 0.00 3.16
1730 1810 5.376625 ACAGTTTGCATTCAGAAGAGGTTA 58.623 37.500 0.00 0.00 0.00 2.85
1787 1868 8.242085 TCATTTGTGAACATAAAACATGCATC 57.758 30.769 0.00 0.00 0.00 3.91
1795 1876 7.039853 TCAGAGGCATCATTTGTGAACATAAAA 60.040 33.333 0.00 0.00 0.00 1.52
1801 1882 4.669318 CATCAGAGGCATCATTTGTGAAC 58.331 43.478 0.00 0.00 0.00 3.18
1806 1888 2.949644 TGAGCATCAGAGGCATCATTTG 59.050 45.455 10.23 0.00 42.56 2.32
1829 1911 7.945134 AGCAAAAACAGTGATAATCAAGACTT 58.055 30.769 0.00 0.00 0.00 3.01
1830 1912 7.516198 AGCAAAAACAGTGATAATCAAGACT 57.484 32.000 0.00 0.00 0.00 3.24
1904 1990 7.288810 AGAGCTCCAATTGTGAACATTAAAA 57.711 32.000 10.93 0.00 0.00 1.52
1916 2002 7.118245 GGGTTCAAATAAAAAGAGCTCCAATTG 59.882 37.037 10.93 6.85 0.00 2.32
1924 2010 5.856986 GTCGAAGGGTTCAAATAAAAAGAGC 59.143 40.000 0.00 0.00 0.00 4.09
1931 2017 7.613585 TGTATGTAGTCGAAGGGTTCAAATAA 58.386 34.615 0.00 0.00 0.00 1.40
1933 2019 6.045072 TGTATGTAGTCGAAGGGTTCAAAT 57.955 37.500 0.00 0.00 0.00 2.32
1979 2217 1.394917 GAAATCGCAATCGTCAGCACT 59.605 47.619 0.00 0.00 36.96 4.40
1987 2225 2.166007 GTCGTTTGGAAATCGCAATCG 58.834 47.619 0.00 0.00 38.80 3.34
1993 2231 3.431912 TGATCTGTGTCGTTTGGAAATCG 59.568 43.478 0.00 0.00 40.19 3.34
1997 2235 4.058124 CTCTTGATCTGTGTCGTTTGGAA 58.942 43.478 0.00 0.00 0.00 3.53
2007 2245 3.446873 AGTCTAGGTGCTCTTGATCTGTG 59.553 47.826 0.00 0.00 30.55 3.66
2008 2246 3.707316 AGTCTAGGTGCTCTTGATCTGT 58.293 45.455 0.00 0.00 30.55 3.41
2022 2260 3.427773 GCTTCTTGGTGTCGTAGTCTAGG 60.428 52.174 0.00 0.00 0.00 3.02
2049 2287 3.748568 ACGATTTCTCCTTGACAAAGCTC 59.251 43.478 0.00 0.00 31.51 4.09
2173 2411 2.300433 CATGATTCATTCGCCCCTTGA 58.700 47.619 0.00 0.00 0.00 3.02
2271 2509 2.161609 CGGGTAAAACATCAAGGCTGTC 59.838 50.000 0.00 0.00 0.00 3.51
2278 2516 4.200874 ACAAGACACGGGTAAAACATCAA 58.799 39.130 0.00 0.00 0.00 2.57
2326 2567 0.788391 CTCGTTCGTAGCAACAACCC 59.212 55.000 0.00 0.00 0.00 4.11
2354 2595 2.159000 AGGGTTAAATGTCCGATCGACC 60.159 50.000 18.66 13.09 41.18 4.79
2362 2603 7.114095 TGATAGGTAACAAGGGTTAAATGTCC 58.886 38.462 0.00 0.00 40.95 4.02
2415 2656 1.002544 CAGGTTCAGGTTCAGGACTCC 59.997 57.143 0.00 0.00 0.00 3.85
2425 2666 1.359168 GTAGGGGAACAGGTTCAGGT 58.641 55.000 13.62 0.62 41.20 4.00
2440 2681 5.832539 ATGAATGGAGATAACAGGGTAGG 57.167 43.478 0.00 0.00 0.00 3.18
2455 2696 8.818141 ACTGTTACGACTTCATATATGAATGG 57.182 34.615 24.77 17.59 44.92 3.16
2461 2702 9.574458 GCATGATACTGTTACGACTTCATATAT 57.426 33.333 0.00 0.00 0.00 0.86
2462 2703 8.027189 GGCATGATACTGTTACGACTTCATATA 58.973 37.037 0.00 0.00 0.00 0.86
2527 2775 3.384668 CACCGTATAAGCATGTCCTCAG 58.615 50.000 0.00 0.00 0.00 3.35
2559 2808 4.952335 GTGTCATCCAAGAGAAAATGGGAT 59.048 41.667 0.00 0.00 38.87 3.85
2564 2813 7.607991 AGATAAACGTGTCATCCAAGAGAAAAT 59.392 33.333 0.00 0.00 0.00 1.82
2592 2842 0.871722 TTCAGATTCGCCACAAACCG 59.128 50.000 0.00 0.00 0.00 4.44
2602 2852 4.158384 CCACCGTTTCAATTTCAGATTCG 58.842 43.478 0.00 0.00 0.00 3.34
2621 2871 0.958382 TACCTGCGCATGGAAACCAC 60.958 55.000 26.07 0.00 35.80 4.16
2641 2891 6.378710 TCTCAACGTGTCCTTCATATCTAG 57.621 41.667 0.00 0.00 0.00 2.43
2657 2910 2.014068 GCCTCCCCATCTTTCTCAACG 61.014 57.143 0.00 0.00 0.00 4.10
2682 2935 0.392863 TGTCCAGGCACATTCATCGG 60.393 55.000 0.00 0.00 0.00 4.18
2730 2989 3.748568 GCTCTATATACAGTGCAAAGGGC 59.251 47.826 0.28 0.00 45.13 5.19
2733 2992 3.430218 GCCGCTCTATATACAGTGCAAAG 59.570 47.826 5.95 0.00 35.30 2.77
2774 3057 2.746277 ACGCCCTTCGCACCATTC 60.746 61.111 0.00 0.00 43.23 2.67
2790 3073 4.096984 CACCAAAAGGCCAAGATATCTCAC 59.903 45.833 5.01 0.00 0.00 3.51
2899 3188 6.625362 TCATCAGTTACTTACTTGCAGAGAG 58.375 40.000 3.37 0.00 33.85 3.20
2913 3202 3.932710 TCATCGCAAACCTCATCAGTTAC 59.067 43.478 0.00 0.00 0.00 2.50
3002 3295 1.126948 TGTGCACCAGACCAGATGGA 61.127 55.000 15.69 0.00 40.51 3.41
3003 3296 0.034767 ATGTGCACCAGACCAGATGG 60.035 55.000 15.69 0.00 43.87 3.51
3004 3297 1.471287 CAATGTGCACCAGACCAGATG 59.529 52.381 15.69 0.00 0.00 2.90
3005 3298 1.074405 ACAATGTGCACCAGACCAGAT 59.926 47.619 15.69 0.00 0.00 2.90
3007 3300 0.594602 CACAATGTGCACCAGACCAG 59.405 55.000 15.69 0.00 0.00 4.00
3008 3301 0.106769 ACACAATGTGCACCAGACCA 60.107 50.000 15.69 0.00 36.98 4.02
3009 3302 0.311790 CACACAATGTGCACCAGACC 59.688 55.000 15.69 0.00 41.89 3.85
3010 3303 3.851620 CACACAATGTGCACCAGAC 57.148 52.632 15.69 0.00 41.89 3.51
3035 3335 6.267471 TCAGTGGCATTAAGGACAAAGAAAAT 59.733 34.615 0.00 0.00 0.00 1.82
3055 3356 1.728971 GAAGACGACTTGGCATCAGTG 59.271 52.381 4.51 0.00 36.39 3.66


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.